Script parameters

There is a universal @parameter notation available across all scripts for declaring inputs and outputs. This approach is preferred to using ImageJ 1.x GenericDialog because it is totally agnostic to the user interface, allowing such scripts to run in a variety of contexts.

Using the script editor

Adding scripts to the Plugins menu

For the script to appear in the ImageJ menus, the following must apply:

".txt" is not a supported script extension

The script file is saved in the ImageJ.app/scripts or the ImageJ.app/plugins/Scripts directory (or a subdirectory thereof).

The script name ends in a supported script extension. For example

".groovy" for groovy,

".js" for javascript,

".py" for jython,

".rb" for jruby,

".clj" for clojure,

".bsh" for beanshell, and

".ijm" for ImageJ 1.x macros.

The script name contains a '_' (underscore) character, e.g. "MyScript_.ijm".

Replace ImageJ.app with Fiji.app

The extension will be stripped and any underscores will be turned into spaces before the script is added to the menus.

Scripts in the top-level ImageJ.app/plugins directory will appear at the bottom of the Plugins menu. Scripts can be placed in other menus by nesting subdirectories, for example placing a script in the ImageJ.app/scripts/File directory will add it to the File menu.

If you aren't able to find your script, you can always run the Command Finder to verify its location (or absence).

Commands added to the menu in the described way can be called from other scripts. Use the macro recorder to get the required code for doing so.

Adding JAR-packaged scripts to the menu

Scripts can be packaged in a JAR file for easier distribution to your colleagues and via [Update Sites]. For this purpose, example-script-collection can be used as the template Maven project.

Inside the example-script-collection jar, the scripts are in ./resources/scripts. and therefore get added to the menu when the JAR is on the classpath (i.e. in ./plugins/ or ./jars/).

ImageJ2 (and therefore Fiji) looks for scripts in subfolders of ./scripts/ as it is already described in the previous section, and for jars in ./jars/. ImageJ1 recognizes plugins and scripts in ./plugins/

Calling a script from another script

There are different ways to call a script from another script.
Generally, the called script is executed in the same thread than the calling script, which means that the calling script will wait that the called script terminates before going on with the rest of the execution.

Using ImageJ1 commands

ImageJ offers the possibility to call a plugin, macro or script within another one.
If the plugin is already part of the Menu, the simple command run(PluginName, string Arguments) (or IJ.run for other scripting languages) as returned by the macro-recorder will work.

However when one wants to call a home-made local macro that is not part of the ImageJ menu, one uses a different command (see below).
Here the example of a mainMacro calling a subMacro.

It is also possible to pass arguments to the subMacro, it works similar to the command line execution.
The subMacro needs to use getArgument() (or IJ.imageJ.getArgs of the ImageJ API) to recover the string of argument passed to it.

The command runMacro works only for ijm macro.
To call a script written in another scripting languages, one should use the runMacroFile(PathToScript, Arguments) (respectively IJ.runMacroFile of the ImageJ API). Still using the getArgument to pass the variables from mainScript to subScript.

This 1st option is however limited to ImageJ1 code style, meaning that one cannot use script parameters, or call any service in subScript.
Luckily ImageJ2 also have is own way to call a script within a script.

Using ImageJ2 command

One can use the ScriptService from scijava to run a script within a script.
Here the example of a mainScript calling a subScript both in Jython.